I have currently boostrapped my model and deployed my jars in my local environment.

I have a production environment on which the content model has already been loaded via the Share UI and is present in the database.

If the content model was created via share UI and resides in alf_data (database), when I bootstrap the same model with additional changes, will the bootstrap override what ever was there in alf_data that was initially uploaded via share UI. If say an aspect already existed would it cause any issues?

If using Model Manager at PROD to include your additional properties is not an option, safer alternative is to download all your uploaded documents against the model to be re-uploader later. Once you have remove the model with Model Manager Tool and re-started your Alfresco with the bootstrapped model.